[Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Duncan Murdoch
murdoch at stats.uwo.ca
Tue Apr 22 19:18:56 CEST 2008
There seem to be nonlinearities in the time-space continuum, so this
message arrived several hours after Martin's, even though both have the
same timestamp. Please test his, and see if you can break it. I'd
guess not, it looks simple enough, but not too simple.
And for the future:
Please test the alpha/beta/RC releases! The change we're talking about
came fairly late in the process, but it was there for the last couple of
weeks. It would be easier for everyone if it had been corrected before
release, rather than after. It was announced on the RSS list, here:
http://developer.r-project.org/blosxom.cgi/R-2-7-branch/NEWS/2008/04/08#n2008-04-08
so it would really have helped if people who rely on special axis
handling by Axis had tested the change after they'd seen that notice.
On 4/22/2008 10:26 AM, Sklyar, Oleg (MI London) wrote:
> Ok, so what's wrong with the following fix for plot(x)
The main thing that's wrong with it is that you don't explain what the
changes are. I can't believe that the error is specific to the POSIXct
class, so it doesn't make sense that changes there would fix it in general.
Duncan Murdoch
> that would
> actually fix what needs to be fixed instead of changing plot.default?
> Fix means reverting plot.default in 2.7.0 to what it was (if testing in
> 2.7.0, copy and paste the OLD plot.default into the .GlobalEnv):
>
> plot.POSIXct <- function(x, y, xlab = "", ...) {
> if (!missing(y)) {
> side = 1
> plotDef <- function(x, y, xaxt, xlab, ...) plot.default(x, y,
> xaxt="n", xlab=xlab, ...)
> plotDef(x, y, xlab=xlab, ...)
> } else {
> side = 2
> plotDef <- function(x, y, yaxt, xlab, ...) plot.default(x, y,
> yaxt="n", xlab=xlab, ...)
> plotDef(seq_along(x), x, xlab=xlab, ...)
> }
> ## trick to remove arguments intended for title() or plot.default()
> axisInt <- function(x, type, main, sub, xlab, ylab, col, lty, lwd,
> xlim, ylim, bg, pch, log, asp, axes, frame.plot,
> ...)
> axis.POSIXct(side, x, ...)
> dots <- list(...)
> axes <- if("axes" %in% names(dots)) dots$axes else TRUE
> xaxt <- if("xaxt" %in% names(dots)) dots$xaxt else par("xaxt")
> if(axes && xaxt != "n") axisInt(x, ...)
> }
>
> plot.POSIXlt <- function(x, y, xlab = "", ...) {
> if (missing(y)) plot.POSIXct(as.POSIXct(x), xlab=xlab, ...)
> else plot.POSIXct(as.POSIXct(x), y=y, xlab=xlab, ...)
> }
>
> And try with:
> x = Sys.time() + runif(100,1,7200)
> plot(x)
> plot(x,1:100)
> plot(1:100,x)
>
> plot(as.POSIXlt(x))
> plot(as.POSIXlt(x),1:100)
> plot(1:100,as.POSIXlt(x))
>
>
> Dr Oleg Sklyar
> Technology Group
> Man Investments Ltd
> +44 (0)20 7144 3803
> osklyar at maninvestments.com
>
>> -----Original Message-----
>> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
>> Sent: 22 April 2008 14:24
>> To: Sklyar, Oleg (MI London)
>> Cc: R-devel at r-project.org
>> Subject: Re: [Rd] graphics::Axis loosing S3/S4 class
>> attributes of 'x' in 2.7.0 RC
>>
>> On 4/22/2008 9:08 AM, Sklyar, Oleg (MI London) wrote:
>> > Duncan,
>> >
>> > looking further, what has changed from 2.6.2 into 2.7.0 are the
>> > following two lines in plot.default, which I think were
>> logical before
>> > and are not really logical now:
>>
>> I believe it is behaving as documented now, so the behaviour
>> is "logical", even if it may not be convenient. In your example
>>
>> x = Sys.time() + runif(100,1,7200) ## time over two hours,
>> POSIXct plot(x, 1:100) plot(1:100, x)
>>
>> the 1st works in 2.6.2 and 2.7.0 and the second only works in 2.6.2.
>> But the change below was designed to fix the case
>>
>> plot(x)
>>
>> which works in 2.7.0 and *not* in 2.6.2, so reverting the
>> change is not the way to address this.
>>
>> Duncan Murdoch
>>
>> >
>> > plot.R: plot.default (2.6.2):
>> > if (axes) {
>> > localAxis(x, side=1, ...)
>> > localAxis(y, side=2, ...)
>> > }
>> >
>> > plot.R: plot.default (2.7.0):
>> > ...
>> > if (axes) {
>> > localAxis(xy$x, side=1, ...)
>> > localAxis(xy$y, side=2, ...)
>> > }
>> >
>> > The fact that xy.coords is called does not really matter.
>> >
>> >
>> > Dr Oleg Sklyar
>> > Technology Group
>> > Man Investments Ltd
>> > +44 (0)20 7144 3803
>> > osklyar at maninvestments.com
>> >
>> >> -----Original Message-----
>> >> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
>> >> Sent: 22 April 2008 13:01
>> >> To: Sklyar, Oleg (MI London)
>> >> Cc: R-devel at r-project.org
>> >> Subject: Re: [Rd] graphics::Axis loosing S3/S4 class attributes of
>> >> 'x' in 2.7.0 RC
>> >>
>> >> On 22/04/2008 7:25 AM, Sklyar, Oleg (MI London) wrote:
>> >> > Following my previous post on S3 method despatch, I put
>> >> debug messages
>> >> > in the code of Axis, Axis.default and plot.default in
>> >> > graphics/R/axis.R and graphics/R/plot.R to print the
>> class of x, at
>> >> > and y on plot. After recompiling R, what I see is that x
>> *lost* its
>> >> > class attribute (at least for classes not known to
>> 'graphics') in
>> >> > Axis, called directly from plot.default and this could be
>> >> the reason
>> >> > why R did not despatch on Axis.MyClass from my previous
>> post. This
>> >> > happens for both S3 and S4 classes as in the code below!
>> >> Funny enough,
>> >> > even "integer" was reset to numeric in Axis...
>> >>
>> >> If you look at plot.default, you'll see it passes x and y through
>> >> xy.coords to get coordinates. That function ends with
>> >>
>> >> return(list(x=as.double(x), y=as.double(y), xlab=xlab, ylab=ylab))
>> >>
>> >> so that's where classes get removed. If you don't want this to
>> >> happen, shouldn't you be defining plot.MyClass, or calling the
>> >> default with axes=F, and then calling Axis on your object yourself?
>> >>
>> >> > Is this really an intended behaviour? It looks very wrong to me!
>> >>
>> >> This is documented: ?plot.default tells you to look at ?xy.coords
>> >> for details of how x and y are handled, and xy.coords says "In any
>> >> other case, the 'x' argument is coerced to a vector and
>> >> returned as *y* component where the resulting 'x' is just the
>> >> index vector '1:n'. In this case, the resulting 'xlab'
>> >> component
>> >> is set to '"Index"'."
>> >>
>> >> Duncan Murdoch
>> >>
>> >> > Thanks,
>> >> > Oleg
>> >> >
>> >> > *** R version 2.7.0 RC (2008-04-20 r45403)
>> >> [/research/osklyar/R-devel]
>> >> > ***
>> >> >> Axis
>> >> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
>> >> > cat("In Axis() class(x)=", class(x), "; class(at)=",
>> class(at),
>> >> > "\n", sep = "")
>> >> > if (!is.null(x))
>> >> > UseMethod("Axis", x)
>> >> > else if (!is.null(at))
>> >> > UseMethod("Axis", at)
>> >> > else axis(side = side, at = at, labels = labels, ...) }
>> >> > <environment: namespace:graphics>
>> >> >> graphics:::Axis.default
>> >> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
>> >> > cat("In Axis.default() class(x)=", class(x), "; class(at)=",
>> >> > class(at), "\n", sep = "")
>> >> > if (is.null(at) && !is.null(x))
>> >> > at = pretty(x)
>> >> > axis(side = side, at = at, labels = labels, ...) }
>> >> > <environment: namespace:graphics>
>> >> >> setClass("MyClass", representation(smth="character"),
>> >> > contains="numeric")
>> >> > [1] "MyClass"
>> >> >> a = new("MyClass", runif(10))
>> >> >> a
>> >> > An object of class "MyClass"
>> >> > [1] 0.773237167 0.548630205 0.987956687 0.212667925 0.337135151
>> >> > 0.112210501
>> >> > [7] 0.007140895 0.972028903 0.443581963 0.536452424 Slot "smth":
>> >> > character(0)
>> >> >> plot(1:10,a)
>> >> > In plot.default() class(x)=integer; class(y)=MyClass In Axis()
>> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> class(x)=numeric;
>> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> plot(a,1:10)
>> >> > In plot.default() class(x)=MyClass; class(y)=integer In Axis()
>> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> class(x)=numeric;
>> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> b = runif(10)
>> >> >> class(b)="AnotherClass"
>> >> >> plot(b,1:10)
>> >> > In plot.default() class(x)=AnotherClass;
>> class(y)=integer In Axis()
>> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> class(x)=numeric;
>> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> plot(1:10)
>> >> > In plot.default() class(x)=integer; class(y)=NULL In Axis()
>> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> class(x)=numeric;
>> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> > Axis.default() class(x)=numeric; class(at)=NULL>
>> >> >> sessionInfo()
>> >> > R version 2.7.0 RC (2008-04-20 r45403) x86_64-unknown-linux-gnu
>> >> >
>> >> > locale:
>> >> >
>> >>
>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=C;LC
>> >> _
>> >> > MO
>> >> >
>> >>
>> NETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_AD
>> >> D
>> >> > RE
>> >> SS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>> >> >
>> >> > attached base packages:
>> >> > [1] stats graphics grDevices utils datasets
>> methods base
>> >> >
>> >> >
>> >> > Dr Oleg Sklyar
>> >> > Technology Group
>> >> > Man Investments Ltd
>> >> > +44 (0)20 7144 3803
>> >> > osklyar at maninvestments.com
>> >> >
>> >> >
>> >> >
>> >>
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